﻿<?xml version="1.0" encoding="utf-8" ?>
<AutomationTest>
  <!-- This node contains the Fasta file information for running Step 4 :PCA BVT test cases. -->
  <EColi500WithZeroError1XPairedReads>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_ZeroError_1x_Paired.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <FixedSeparation>0</FixedSeparation>
    <MUMLength>3</MUMLength>
    <MinimumScore>2</MinimumScore>
    <SeparationFactor>-1</SeparationFactor>
    <CountOfExpectedSequences>1</CountOfExpectedSequences>
    <ExpectedSequence>agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacctggtggcgatgattgaaaaaaccat</ExpectedSequence>
  </EColi500WithZeroError1XPairedReads>    
  
  <!-- This node contains the Fasta file information for running Comparitive Assembly Step 1-5 :PCA BVT test cases. -->
  <FastaWithOneLineSequence>
    <FilePath1>TestUtils\ComparativeTestData\Simple_Fasta_DNA_Ref.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Simple_Fasta_DNA_Reads.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequence>ATGCAGTA</ExpectedSequence>
    <MUMLength>3</MUMLength>
    <KmerLength>3</KmerLength>
  </FastaWithOneLineSequence>
  <FastaWithOneLineSequenceNodeWithErrors>
    <FilePath1>TestUtils\ComparativeTestData\Simple_Fasta_DNA_RefWith_72bp.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Simple_Fasta_DNA_ReadsWithErrors_.001_1.fa</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>3</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>ATGCAGTAATGCAGTAATGCAGTAATGCAGTAATGCAGTAATGCAGTAATGCAGTAATGCAGTAATGCAGTA</ExpectedSequence>         
  </FastaWithOneLineSequenceNodeWithErrors>
  <FastaOneLineSequenceWithAddition>
    <ReferenceSequences>ATGCAGTAAAATA</ReferenceSequences>
    <SearchSequences>ATGCGAT,ACGTAAT</SearchSequences>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>3</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>ATGCGTAAAAT</ExpectedSequence>
  </FastaOneLineSequenceWithAddition>
  <FastaOneLineSequenceWithDeletion>
    <ReferenceSequences>ATGCAGTAATATGCGA</ReferenceSequences>
    <SearchSequences>ATGGTAG,AGTGTAT</SearchSequences>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>3</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>AGTAATGTATG</ExpectedSequence>    
  </FastaOneLineSequenceWithDeletion>
  <SimpleFasta>
    <FilePath1>TestUtils\ComparativeTestData\PCASimpleDnaFile1.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\PCASimpleDnaFile2.fasta</FilePath2>
    <ReferenceSequences>AGAAAAGTTTTCA</ReferenceSequences>
    <SearchSequences>AAAAG,TTTT</SearchSequences>
    <AlphabetName>Protein</AlphabetName>
    <CountOfExpectedSequences>1</CountOfExpectedSequences>
    <ExpectedSequence>AAAAGTTTT</ExpectedSequence>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>2</MinimumScore>
    <SeparationFactor>-1</SeparationFactor>
    <MUMLength>3</MUMLength>
    <ConsensusWithNullDelta>Value cannot be null.Parameter name: alignmentBetweenReferenceAndReads</ConsensusWithNullDelta>    
  </SimpleFasta>
  <SequenceWithErrorsReads>    
    <FilePath1>TestUtils\ComparativeTestData\Multi_Seq_Medium_Size.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Multi_Seq_Search_Medium_Size.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>    
    <MUMLength>5</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>TGSMRAWKKYTWTWRRRAMWWWARRYYMWWAMYARYWYMKRKRWWARWMRWTWATMTRRMTRKCWAAWMCRRRRTWKYWTTWAYWRTWWATWRWRAWAKASYKWWWRYGGWTKKTWACMWWMYWKKRRSARRGARAAAWATWWWAATTWTWMYWKARKMYMWAAARAARWYRKAWWRRARARWAWKWKKWRWWAWWTWRKCWYAWAACCTTGSKWWWAAAGRTKTWWWKRRRKWWWRSRWWRKMMAAYWAAWRATWWARAKMWAAWWMYTAKWRRTTTKRMTSAWTTSCAWTWRRGRWWAWYRWWWWRAWTMKWTMSAMMATWMMGMTKWYSTWRKGWTAMWAKMAYWYSKWWRGWATTWRRRRMAKGCAWWWTASTAATMYKMARMKGGGAYRWWWMMTMTAAKRTATKWKKTARRYRAWKKRRARARYKRWARMRRWAWAATMKAAWWARAAAGMWAKRGCSMWTWYTAKARSRAMSYWTWRWRWKWWTGGTTATCTAATATATTGGCCCAATTCTATATAAAAAAGATAGCTTTTGGATTTTTTAAAATAAAAAATTTGAGAAGAATAAAGAATGGCAAAAAGCAATGGTATTTAAAAGGATATGCTATGGGGGAGCCTTATTCTATGGAGAAGCATAATTTTAAAAAAGAAGTAAAAGCTGTAACATGGCATGGTTTAGATATTAAAAGGGAAGG</ExpectedSequence>
  </SequenceWithErrorsReads>

  <!--This node cotains test data for Zero error's 10x coverage, without paired reads-->
  <SequenceWithZeroErrorsAnd10XCoverage>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_ZeroError_10x.fa</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>15</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacctggtggcgatgattgaaaaaaccat</ExpectedSequence>
  </SequenceWithZeroErrorsAnd10XCoverage>

  <!--This node cotains test data for Zero error's 1x coverage, without paired reads-->
  <SequenceWithZeroErrorsAnd1XCoverage>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_ZeroError_1x.fa</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>6</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>AAAATTAAAACACAGAAAAAAAATTAAAATTTTATTGAACGTTTTCAAGCAATGCATTAAAAATTCTGCAATATGTCTCTGCACAGACATGAAACGCATCATTCTGACCAATATAGGCATGCCCGCACCTGGCAGGTGGCCACGGTGGCGTCCTCTCTGCCCGTGTCTGATAGGTTACCTGCCGTGAGTGAAGTTTGATTGAAAAATGCGGGCTTGCGGGCTGACTTCTGAACTTTTTTC</ExpectedSequence>
  </SequenceWithZeroErrorsAnd1XCoverage>

  <!--This node cotains test data for Zero error's 10x coverage, with paired reads-->
  <SequenceWithZeroErrorsAnd10XCoveragePaired>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_ZeroError_10x_Paired.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>15</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacctggtggcgatgattgaaaaaaccat</ExpectedSequence>
  </SequenceWithZeroErrorsAnd10XCoveragePaired>

  <!--This node cotains test data for Zero error's 1x coverage, with paired reads-->
  <SequenceWithZeroErrorsAnd1XCoveragePaired>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_ZeroError_1x_Paired.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>6</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>agcttttcattctgactgcaacgggcaatatgtctctgtgtggattaaaaaaagagtgtctgatagcagcttctgaactggttacctgccgtgagtaaattaaaattttattgacttaggtcactaaatactttaaccaatataggcatagcgcacagacagataaaaattacagagtacacaacatccatgaaacgcattagcaccaccattaccaccaccatcaccattaccacaggtaacggtgcgggctgacgcgtacaggaaacacagaaaaaagcccgcacctgacagtgcgggctttttttttcgaccaaaggtaacgaggtaacaaccatgcgagtgttgaagttcggcggtacatcagtggcaaatgcagaacgttttctgcgtgttgccgatattctggaaagcaatgccaggcaggggcaggtggccaccgtcctctctgcccccgccaaaatcaccaaccacctggtggcgatgattgaaaaaaccat</ExpectedSequence>
  </SequenceWithZeroErrorsAnd1XCoveragePaired>                 

  <!-- This node contains the Fasta file information for running Comparitive Assembly Step 1-5 :PCA P1 test cases. -->
  <SingleRnaNucmerSequence>
    <FilePath1>TestUtils\ComparativeTestData\SingleRnaSequence.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\SingleRnaSequenceReads100XWith.001Error_1.fa</FilePath2>
    <AlphabetName>Rna</AlphabetName>
    <MUMLength>6</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>Will be taken from current</ExpectedSequence>
  </SingleRnaNucmerSequence>    
  <LargeSequenceWithDeletedReads>
    <FilePath1>TestUtils\ComparativeTestData\LargeSize_DNA_Ref.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\LargeSize_DNA_Reads_WithDeletion.fa</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>10</MUMLength>
    <KmerLength>5</KmerLength>
    <ExpectedSequence>TTAAAAAATACAAAAGGTTTATTAGATATAATAAAAAAGAAAGAGGAAAATTATARAKRWRAAAGAGAATTTGTTTTGGGTTTACAAAAAAGAGATGAAGAGAAAATACAAAAGTTTTTAGCTAGGAAAATTAAATAGAGTTTCCATTAAAAGAAAGAAAAAGCACTATTATATCAGCAACAATATTGAAAAAATTAGAAGAAAAACWAWAAWRRATACAAAATTAGAAAATTTAAAAAAATACAAAAAAAATTAGAGAGAAATAAAAATAAAAATAGAAATAGAGTTTTAAATAAAAATTTATTGAAGAAAAAAAAAGCAAAAGAATTTGAAAAAAAATAGAATATTTGTTAGCAAAAAAGAGAACAATAAAATTTTATAGTAGATGACAAAATAGATAAAAGTGTTCAAATAAAAAATGCGATATATGAAAGAGAAAGAGCTAGATTGAAAAAATAAATACAAAAACGAATATGATTTTATGCTAATTTGGGTTTAGAAAGAACTAAAACAATTTAAAAAATTGTTAAAATACAAACATATCTTTAGTACAAAGCTAAATAAAAATAAGATATAATTGAATAAAATTTGAGAATTTGAAATAAAAAGGTTATTGAAGAAAAAGGCAAAATGAAAGGCAAAGGTAAAAATACAATTACAAAACAAAGCTAATTTATGCTAAAAAATTTGAAATAAAACAAACAATTTATATCTATTCTTAAAAGTGTTGTAGAAAAAATAGAACACCCAAACTAATAAAAAAAGTAATAAAATTGAAAAAAGAATGTTGAAATAAAAGAAATTGTTTGTAAAACAATTTTAGAAAAAAGAAATTCTATTCTAACAAAAAAAGAACTATTTGCAAAAATTGTCAATAAAATTTATATGAAAGTACAAAATTCTAACAAAAAAATTCCAAAAG</ExpectedSequence>
    </LargeSequenceWithDeletedReads>
  <LargeSequenceWithAddedReads>
    <FilePath1>TestUtils\ComparativeTestData\LargeSize_DNA_Ref.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\LargeSize_DNA_Reads_WithAddition.fa</FilePath2>
    <MUMLength>15</MUMLength>
    <KmerLength>5</KmerLength>
    <AlphabetName>Dna</AlphabetName>
    <ExpectedSequence>AAAGAGAAATACAAAAATAATAAAAGAGATCAAATTCGTTTTACCAAAAGGTAAAAATAAAAAGATATAGATGATAAAAT</ExpectedSequence>
  </LargeSequenceWithAddedReads>
  <EcoliDataWithErrors>
    <FilePath1>TestUtils\ComparativeTestData\EColi-NC_000913-Ref.bd.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\EColi-NC_000913.bd_1xWithError-Reads_1.fa</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>30</MUMLength>
    <KmerLength>5</KmerLength>
    <ExpectedSequence>TestUtils\ComparativeTestData\EcoliDataWithErrors_output.txt</ExpectedSequence>    
  </EcoliDataWithErrors>
  
  <!-- Following nodes contain Test data details: Without errors-->
  <EcoliDataWithZeroErrorsNonPaired>
    <FilePath1>TestUtils\ComparativeTestData\EColi-NC_000913-Ref.bd.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\EColi-NC_000913-Ref.bd.1X.NonPairedReads.fa</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>15</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>TestUtils\ComparativeTestData\EcoliDataWithZeroErrorsNonPaired_output.txt</ExpectedSequence>
  </EcoliDataWithZeroErrorsNonPaired>
  <EcoliDataWithZeroErrorsPaired>
    <FilePath1>TestUtils\ComparativeTestData\EColi-NC_000913-Ref.bd.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\EColi-NC_000913-Ref.bd.1X.PairedReads.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <MUMLength>30</MUMLength>
    <KmerLength>3</KmerLength>
    <ExpectedSequence>TestUtils\ComparativeTestData\EcoliDataWithZeroErrorsPaired_output.txt</ExpectedSequence>
  </EcoliDataWithZeroErrorsPaired>
  
  <!-- This node contains the Fasta file information for running Comparitive Assembly Step 2 :PCA BVT test cases. -->
  <RepeatResolution>
    <FilePath1>TestUtils\ComparativeTestData\Simple_Fasta_DNA_Ref.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Simple_Fasta_DNA_Reads.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <ReferenceSequences>ATGCAGTA</ReferenceSequences>
    <SearchSequences>ATGC,AGTA</SearchSequences>
    <ExpectedSequence>ATGCAGTA</ExpectedSequence>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <SeparationFactor>0</SeparationFactor>
    <MUMLength>3</MUMLength>
    <FirstSequenceEndNode>3,7</FirstSequenceEndNode>
    <FirstSequenceStart>0,4</FirstSequenceStart>
    <DeltasNode>0,0</DeltasNode>
    <SecondSequenceStartNode>0,0</SecondSequenceStartNode>
    <SecondSequenceEndNode>3,3</SecondSequenceEndNode>    
    <ResolveAmbiguityWithNullDeltas>Value cannot be null.Parameter name: alignmentBetweenReferenceAndReads</ResolveAmbiguityWithNullDeltas>
  </RepeatResolution>  
  <!--This node cotains test data for Zero error's 1x coverage, with paired reads-->
  <RepeatResolutionWithPairedReads>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_ZeroError_1x_Paired.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <SeparationFactor>0</SeparationFactor>
    <MUMLength>3</MUMLength>
    <FirstSequenceEndNode>39,74,109,144,179,214,249,284,319,354,389,424,459,494,499</FirstSequenceEndNode>
    <FirstSequenceStart>0,35,70,105,140,175,210,245,280,315,350,385,420,455,460</FirstSequenceStart>
    <DeltasNode>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0</DeltasNode>
    <SecondSequenceStartNode>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0</SecondSequenceStartNode>
    <SecondSequenceEndNode>39,39,39,39,39,39,39,39,39,39,39,39,39,39,39</SecondSequenceEndNode>
  </RepeatResolutionWithPairedReads>
  <!--This node cotains test data With error's 1x coverage, with paired reads and insertion and deletion rate being 0.001-->
  <RepeatResolutionWithErrorsInPairedReads>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_WithError_1x_Paired.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <SeparationFactor>0</SeparationFactor>
    <MUMLength>3</MUMLength>
    <FirstSequenceEndNode>39,74,109,144,179,214,248,284,124,320,354,389,424,459,494,499</FirstSequenceEndNode>
    <FirstSequenceStart>0,35,70,105,140,175,210,245,121,280,315,350,385,420,455,460</FirstSequenceStart>
    <DeltasNode>0,0,0,0,0,0,17,0,0,7,0,0,0,0,0,0</DeltasNode>
    <SecondSequenceStartNode>0,0,0,0,0,0,0,0,4,0,0,0,0,0,0,0</SecondSequenceStartNode>
    <SecondSequenceEndNode>39,39,39,39,39,39,39,39,7,39,39,39,39,39,39,39</SecondSequenceEndNode>
  </RepeatResolutionWithErrorsInPairedReads>
  <!-- This node contains the Fasta file information for running Comparitive Assembly Step 3 :PCA BVT test cases. -->
  <RefineLayout>
    <FilePath1>TestUtils\ComparativeTestData\Simple_Fasta_DNA_Ref.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Simple_Fasta_DNA_Reads.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <SeparationFactor>0</SeparationFactor>
    <MUMLength>3</MUMLength>
    <ReferenceSequences>ATGCAGTA</ReferenceSequences>
    <SearchSequences>ATGC,AGTA</SearchSequences>
    <ExpectedSequence>ATGCAGTA</ExpectedSequence>    
    <RefineLayoutWithNullDeltas>Value cannot be null.Parameter name: orderedDeltas</RefineLayoutWithNullDeltas>
    <FirstSequenceEndNode>3,7</FirstSequenceEndNode>
    <FirstSequenceStart>0,4</FirstSequenceStart>
    <DeltasNode>0,0</DeltasNode>
    <SecondSequenceStartNode>0,0</SecondSequenceStartNode>
    <SecondSequenceEndNode>3,3</SecondSequenceEndNode>
  </RefineLayout>
  <!--This node cotains test data for Zero error's 1x coverage, with paired reads-->
  <RefineLayoutWithPairedReads>
    <FilePath1>TestUtils\ComparativeTestData\Ecoli.500.fasta</FilePath1>
    <FilePath2>TestUtils\ComparativeTestData\Ecoli.500_ZeroError_1x_Paired.fasta</FilePath2>
    <AlphabetName>Dna</AlphabetName>
    <FixedSeparation>0</FixedSeparation>
    <MinimumScore>0</MinimumScore>
    <SeparationFactor>0</SeparationFactor>
    <MUMLength>3</MUMLength>
    <FirstSequenceEndNode>39,74,109,144,179,214,249,284,319,354,389,424,459,494,499</FirstSequenceEndNode>
    <FirstSequenceStart>0,35,70,105,140,175,210,245,280,315,350,385,420,455,460</FirstSequenceStart>
    <DeltasNode>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0</DeltasNode>
    <SecondSequenceStartNode>0,0,0,0,0,0,0,0,0,0,0,0,0,0,0</SecondSequenceStartNode>
    <SecondSequenceEndNode>39,39,39,39,39,39,39,39,39,39,39,39,39,39,39</SecondSequenceEndNode>
  </RefineLayoutWithPairedReads>
</AutomationTest>
